A new report from the National Treatment Purchase Fund says that overall waiting lists are down, but 1,846 adults and children are still waiting more than a year for surgery.
The total number of patients waiting for surgery alone is over 15,000.
The figures also reveal that over 3,600 patients are waiting more than three months for diagnostic tests.
Over half of these involve a colonoscopy, which is a simple but important test for cancer.
One third of those waiting for these scopes are patients of two hospitals: Letterkenny General Hospital and Tallaght Hospital.
Overall, patients in the northwest of the country are waiting the longest for surgery.
Of the 1,846 patients waiting over a year for an operation, most are patients of Letterkenny General (right), Sligo General Hospital, Children's University Hospital, Temple Street, Mid Western Regional Hospital in Limerick and Cork University Hospital.
Chief Executive of the NTPF Pat O'Byrne said there are still too many patients waiting needlessly for treatment.
He said the NTPF has the budget and the capacity to arrange treatment for these patients and will be working with the hospitals to ensure they get referred and treated.
The Irish Patients' Association has said it is unacceptable that 531 public patients have to wait an average of three months and up to five months for a coronary angiogram.
While welcoming a reduction in the average waiting time for surgery, Stephen McMahon of the IPA said 60% of patients waiting more than 12 months were on the lists at just five hospitals.
Mr McMahon also expressed concern that the NTPF has no significant increase in its budget for 2009.
Meanwhile, Chief Executive of the HSE Professor Brendan Drumm has said that the programme to spend more money in treating patients in the community will further reduce hospital waiting times.
He said that every year the HSE provides day case and inpatient care to more than 1m people and the overall waiting times for this care is coming down.
